\chapter{Conclusion}

In this chapter we conclude this thesis. We have implemented a LIMS for handling the order process and general management of heavy peptides at PROBE, a system that has shown itself as an improvement to the workflow for handling heavy peptides.

\section{Achievements}

The HP LIMS project was conceived by PROBE during the fall of 2010, as more and more heavy peptides were procured for the use in research experiments in the laboratory. A need for an information system that was capable of organizing and storing data about these heavy peptides, and generally aid in some of the cumbersome processes involved in their workflow for handling heavy peptides, arose as the amount of heavy peptide data increased. Key concepts in HP LIMS include \textit{peptide sequence validation}, \textit{automatic order generation}, \textit{organization of peptides} within both orders and experiments, and \textit{a long-term, central storage scheme}.

HP LIMS has been in development for approximately 18 months, and has been gradually introduced in the workflow for handling heavy peptides at PROBE. By bringing HP LIMS into existence PROBE has acquired an information system that provides a central, long-term storage solution for heavy peptide data that can be accessed from any location in a secure manner. A mutually agreed upon format for storing the heavy peptide data has been conceived, and HP LIMS provides tools for auto-generating as much data as possible in this general format.

Standardization of processes has been an important focus in the development process, and this focus has lead to increased efficiency in the execution of previously cumbersome tasks. Creating and building new orders for purchasing heavy peptides was such a task. Automatizing much of the work previously performed manually, and automatically fetching peptide information from external resources such as UniProt, and storing this information in the mutually agreed upon format, has greatly reduced the time spent on creating such orders. As mentioned in Chapter~\ref{chap:existingSystem}, approximately 24 working hours was spent on each order. This time has been reduced to approximately 8 hours after the introduction of HP LIMS.

At the same time as reducing the time spent on creating each order, the risk of introducing human errors in sequences has been drastically reduced by auto-generating orders and validating each sequence entered into an order programmatically according to the rule set specified by PROBE. Entering sequences containing invalid amino acid representations is not possible in HP LIMS, and sequences are only allowed in an order if they conform to the rule set.

\section{Concluding remark}

Designed for long-term storage and quick and simple retrieval of heavy peptide data, HP LIMS has shown itself to be a useful and welcome addition to PROBE. It is a system that is easily extendable, and the use of the Vaadin framework ensures that it is simple to create new user interface components and views in the further development of the application.

\section{Future work}
\label{sec:futureWork}

In this section we present issues that should be resolved in future versions of HP LIMS in order to improve the user experience and general usefulness of the application.

\begin{itemize}
	\item \textit{Automatic backup}: To secure the integrity of the data stored in the database and support the long-term storage scheme by performing regular backups of the database, is an important feature that should be added to HP LIMS in the near future. Possible solutions to create this scheme can be to implement support for scheduled jobs in the application, e.g., by using the enterprise-app\footnote{Released May 2012. URL: https://vaadin.com/directory\#addon/enterprise-app} add-on for Vaadin, which provides automatic configuration and startup of Quartz\footnote{http://quartz-scheduler.org} for scheduled job execution, or by scheduling a cron\footnote{http://en.wikipedia.org/wiki/Cron} job on the server (if the operating system supports cron jobs). Database backups should be stored in a different location from the server.

	\item \textit{Extended support for species}: As mentioned in Chapter~\ref{chap:implementation} the current implementation filters out BLAST results from proteins belonging to other species than human. Later versions of HP LIMS should allow customization of BLAST search parameters, and additional filtering performed after the BLAST search, to accept additional organisms and species. Support for additional species is needed if one works on a project that does not relate to the human species.

	\item \textit{Rule settings}: Users should be able to administer rules through the \textit{Settings} tab, thus a view for rule settings should be added to this tab. The rule creation component described in Section~\ref{subsec:addingPeptides} should be moved from the \textit{Select Sequence Validation Rules} window to this view, and a possibility to also activate/deactivate rules should be present in both the \textit{Select Sequence Validation Rules} window and in the rule settings view. This change will improve the overall usability of the application by making the rule settings more available to the user.
	
	\item \textit{Increase BLAST threshold value}: When short peptide sequences are submitted for BLAST search to UniProt, results found might not be considered statistically significant by the search tool, and hence not returned. As mentioned in Section~\ref{subsec:blast} the threshold for which results are considered statistically significant may be increased in the BLAST search tool provided on UniProt's web pages, and the UniProtJAPI also has functionality embedded to increase this threshold. However, when changing threshold values in the UniProtJAPI we encountered a bug which does not allow for submitting a BLAST job with increased threshold values to UniProt. This issue should be further explored upon and solved in later versions of HP LIMS.

	\item \textit{Advanced search}: A more advanced search feature should be added. Currently, only peptide sequence, name and UniProt accession number are searchable fields, and currently \texttt{Peptide} is the only a searchable entity type. As the application grows and the number of fields connected to each entity type in the database increases, the need for a more comprehensive search feature that is capable of searching across entity types is needed.

	\item \textit{Import existing data from Google Drive}: Data from the temporary spreadsheet should be imported to HP LIMS. When this task has been achieved it should also be possible to edit this data and to add similar data to peptides already present in the HP LIMS database.
\end{itemize}